# ========= [INFO] ==========
# Mut inCB: not accepter mutation in BC
# Mut inMS: 2
# ReadIn  : /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.unmapped.bam
# seq_deb : AGTCGTG
# seq_fin : CGTGG
# MS_seq : AT
# excl : C,G
# nom  : AT15
# =============================
#
#-------------- Filt ------------------
# condiGrep: AGTC.TG[ATCGN]+ATATATATAT[ATCGN]+.GTGG|AGTC.TG[ATCGN]+ATATATATAT[ATCGN]+C.TGG|AGTC.TG[ATCGN]+ATATATATAT[ATCGN]+CG.GG|AGTC.TG[ATCGN]+ATATATATAT[ATCGN]+CGT.G|AGTC.TG[ATCGN]+ATATATATAT[ATCGN]+CGTG.|AGTCG.G[ATCGN]+ATATATATAT[ATCGN]+.GTGG|AGTCG.G[ATCGN]+ATATATATAT[ATCGN]+C.TGG|AGTCG.G[ATCGN]+ATATATATAT[ATCGN]+CG.GG|AGTCG.G[ATCGN]+ATATATATAT[ATCGN]+CGT.G|AGTCG.G[ATCGN]+ATATATATAT[ATCGN]+CGTG.|AGTCGT.[ATCGN]+ATATATATAT[ATCGN]+.GTGG|AGTCGT.[ATCGN]+ATATATATAT[ATCGN]+C.TGG|AGTCGT.[ATCGN]+ATATATATAT[ATCGN]+CG.GG|AGTCGT.[ATCGN]+ATATATATAT[ATCGN]+CGT.G|AGTCGT.[ATCGN]+ATATATATAT[ATCGN]+CGTG.
# condiGrep Rev-Compt: .CACG[NCGAT]+ATATATATAT[NCGAT]+.ACGACT|C.ACG[NCGAT]+ATATATATAT[NCGAT]+.ACGACT|CC.CG[NCGAT]+ATATATATAT[NCGAT]+.ACGACT|CCA.G[NCGAT]+ATATATATAT[NCGAT]+.ACGACT|CCAC.[NCGAT]+ATATATATAT[NCGAT]+.ACGACT|.CACG[NCGAT]+ATATATATAT[NCGAT]+C.CGACT|C.ACG[NCGAT]+ATATATATAT[NCGAT]+C.CGACT|CC.CG[NCGAT]+ATATATATAT[NCGAT]+C.CGACT|CCA.G[NCGAT]+ATATATATAT[NCGAT]+C.CGACT|CCAC.[NCGAT]+ATATATATAT[NCGAT]+C.CGACT|.CACG[NCGAT]+ATATATATAT[NCGAT]+CA.GACT|C.ACG[NCGAT]+ATATATATAT[NCGAT]+CA.GACT|CC.CG[NCGAT]+ATATATATAT[NCGAT]+CA.GACT|CCA.G[NCGAT]+ATATATATAT[NCGAT]+CA.GACT|CCAC.[NCGAT]+ATATATATAT[NCGAT]+CA.GACT
#--------------------------------------
module load picard/2.8.2
> java -jar /env/gfs/apps/picard/2.8.2/picard.jar SortSam I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.unmapped.sam O=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.unmapped.sort.sam SORT_ORDER=queryname 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.unmapped.bam ]
